Search results for: probability density function.

Authors: Parikshit Dutta, Mathieu Saujot, Elise Arnaud, Benoit Lefevre, Emmanuel Prados

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In this work, propagation of uncertainty during calibration process of TRANUS, an integrated land use and transport model (ILUTM), has been investigated. It has also been examined, through a sensitivity analysis, which input parameters affect the variation of the outputs the most. Moreover, a probabilistic verification methodology of calibration process, which equates the observed and calculated production, has been proposed. The model chosen as an application is the model of the city of Grenoble, France. For sensitivity analysis and uncertainty propagation, Monte Carlo method was employed, and a statistical hypothesis test was used for verification. The parameters of the induced demand function in TRANUS, were assumed as uncertain in the present case. It was found that, if during calibration, TRANUS converges, then with a high probability the calibration process is verified. Moreover, a weak correlation was found between the inputs and the outputs of the calibration process. The total effect of the inputs on outputs was investigated, and the output variation was found to be dictated by only a few input parameters.

Keywords: Uncertainty propagation, sensitivity analysis, calibration under uncertainty, hypothesis testing, integrated land use and transport models, TRANUS, Grenoble.

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Authors: Shanxiong Chen, Xu Han, Xiaolong Wang, Hui Ma

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Yi is an ethnic group mainly living in mainland China, with its own spoken and written language systems, after development of thousands of years. Ancient Yi is one of the six ancient languages in the world, which keeps a record of the history of the Yi people and offers documents valuable for research into human civilization. Recognition of the characters in ancient Yi helps to transform the documents into an electronic form, making their storage and spreading convenient. Due to historical and regional limitations, research on recognition of ancient characters is still inadequate. Thus, deep learning technology was applied to the recognition of such characters. Five models were developed on the basis of the four-layer convolutional neural network (CNN). Alpha-Beta divergence was taken as a penalty term to re-encode output neurons of the five models. Two fully connected layers fulfilled the compression of the features. Finally, at the softmax layer, the orthographic features of ancient Yi characters were re-evaluated, their probability distributions were obtained, and characters with features of the highest probability were recognized. Tests conducted show that the method has achieved higher precision compared with the traditional CNN model for handwriting recognition of the ancient Yi.

Keywords: Recognition, CNN, convolutional neural network, Yi character, divergence.

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Authors: Meryem Elif Çelebi Yakartepe, Ayşe Betül Gökarslan

Abstract:

Sustainable architecture is an approach which accepts the climatic and tomographic data as a necessary preliminary data package by favoring the relationship between human and nature and which strives to use the sources economically. The reflection of sustainable architecture approach to preservation - restoration discipline is including the architectural inheritance to daily life with its unique or new function by restoring it.

The restoration decisions of Yılan Kırkan Fountain in Isparta province of Turkey is a good example of the works of sustainable architecture and the preservation of architectural inheritance. It is aimed that Yılan Kırkan Fountain, which is desolate nowadays with no function, to be restored by the local authorities and university, included in the daily life and continue its function.

Keywords: Conservation and Restoration, Sustainable Architecture, Movement Technique, Isparta Yılan Kırkan Fountain.

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Authors: A. Bakhtiar, B. Purwanggono, N. Metasari

Abstract:

PT XYZ is a bottled drinking water company. To preserve production resources owned by the company so that the resources could be utilized well, it has implemented maintenance management system, which has important role in company's profitability, and is one of the factors influenced overall company's performance. Yet, up to now the company has never measured maintenance activities' contribution to company's performance. Performance evaluation is done according to adapted Balanced Scorecard model fitted to maintenance function context. This model includes six perspectives: innovation and growth, production, maintenance, environment, costumer, and finance. Actual performance measurement is done through Analytic Hierarchy Process and Objective Matrix. From the research done, we can conclude that the company's maintenance function is categorized in moderate performance. But, there are some indicators which has high priority but low performance, which are: costumers' complain rate, work lateness rate, and Return on Investment.

Keywords: Maintenance, performance, balanced scorecard, objective matrix.

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Authors: Andre Slonopas, Warren Thompson, Zona Kostic

Abstract:

Obfuscation is one of the most useful tools to prevent network compromise. Previous research focused on the obfuscation of the network communications between external-facing edge devices. This work proposes the use of two edge devices, external and internal facing, which communicates via private IPv4 addresses in a software-defined pseudo-random IP hopping. This methodology does not require additional IP addresses and/or resources to implement. Statistical analyses demonstrate that the hopping surface must be at least 1e3 IP addresses in size with a broad standard deviation to minimize the possibility of coincidence of monitored and communication IPs. The probability of breaking the hopping algorithm requires a collection of at least 1e6 samples, which for large hopping surfaces will take years to collect. The probability of dropped packets is controlled via memory buffers and the frequency of hops and can be reduced to levels acceptable for video streaming. This methodology provides an impenetrable layer of security ideal for information and supervisory control and data acquisition systems.

Keywords: Moving Target Defense, cybersecurity, network security, hopping randomization, software defined network, network security theory.

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Authors: Sayed Amir Hamzeh Mirkheshti

Abstract:

Offshore wind energy as a strategic renewable energy, has been growing rapidly due to availability, abundance and clean nature of it. On the other hand, budget of this project is incredibly higher in comparison with other renewable energies and it takes more duration. Accordingly, precise estimation of time and cost is needed in order to promote awareness in the developers and society and to convince them to develop this kind of energy despite its difficulties. Occurrence risks during on project would cause its duration and cost constantly changed. Therefore, to develop offshore wind power, it is critical to consider all potential risks which impacted project and to simulate their impact. Hence, knowing about these risks could be useful for the selection of most influencing strategies such as avoidance, transition, and act in order to decrease their probability and impact. This paper presents an evaluation of the feasibility of 500 MV offshore wind project in the Persian Gulf and compares its situation with uncertainty resources and risk. The purpose of this study is to evaluate time and cost of offshore wind project under risk circumstances and uncertain resources by using Monte Carlo simulation. We analyzed each risk and activity along with their distribution function and their effect on the project.

Keywords: Wind energy project; uncertain resources; risks; Monte Carlo simulation.

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Authors: Christiono Utomo, Arazi Idrus, Isnanto, Annisa Nugraheni, Farida Rahmawati

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A Negotiation Support is required on a value-based decision to enable each stakeholder to evaluate and rank the solution alternatives before engaging into negotiation with the other stakeholders. This study demonstrates a process of negotiation support model for selection of a building system from value-based design perspective. The perspective is based on comparison of function and cost of a building system. Multi criteria decision techniques were applied to determine the relative value of the alternative solutions for performing the function. A satisfying option game theory are applied to the criteria of value-based decision which are LCC (life cycle cost) and function based FAST. The results demonstrate a negotiation process to select priorities of a building system. The support model can be extended to an automated negotiation by combining value based decision method, group decision and negotiation support.

Keywords: NSS, Value-based, Decision, Construction.

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Authors: E. G. Bautista, J. M. Reyes, O. Bautista, J. C. Arcos

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In this work, we analyze the deformation of surface waves in shallow flows conditions, propagating in a channel of slowly varying cross-section. Based on a singular perturbation technique, the main purpose is to predict the motion of waves by using a dimensionless formulation of the governing equations, considering that the longitudinal variation of the transversal section obey a power-law distribution. We show that the spatial distribution of the waves in the varying cross-section is a function of a kinematic parameter,κ , and two geometrical parameters εh and w ε . The above spatial behavior of the surface elevation is modeled by an ordinary differential equation. The use of single formulas to model the varying cross sections or transitions considered in this work can be a useful approximation to natural or artificial geometrical configurations.

Keywords: Surface waves, Asymptotic solution, Power law function, Non-dispersive waves.

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Authors: Zeinab Jokar, Mohammad Reza Moslemi

Abstract:

In this work, we study the behavior of introducing atomic size vacancy in a graphene nanoribbon superlattice. Our investigations are based on the density functional theory (DFT) with the Local Density Approximation in Atomistix Toolkit (ATK). We show that, in addition to its shape, the position of vacancy has a major impact on the electrical properties of a graphene nanoribbon superlattice. We show that the band gap of an armchair graphene nanoribbon may be tuned by introducing an appropriate periodic pattern of vacancies. The band gap changes in a zig-zag manner similar to the variation of band gap of a graphene nanoribbon by changing its width.

Keywords: Antidot, Atomistix ToolKit, Superlattice, Vacancy.

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Authors: Yi Yu, Lin Ma, Yong Sun, Yuantong Gu

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This paper presents a novel method for remaining useful life prediction using the Elliptical Basis Function (EBF) network and a Markov chain. The EBF structure is trained by a modified Expectation-Maximization (EM) algorithm in order to take into account the missing covariate set. No explicit extrapolation is needed for internal covariates while a Markov chain is constructed to represent the evolution of external covariates in the study. The estimated external and the unknown internal covariates constitute an incomplete covariate set which are then used and analyzed by the EBF network to provide survival information of the asset. It is shown in the case study that the method slightly underestimates the remaining useful life of an asset which is a desirable result for early maintenance decision and resource planning.

Keywords: Elliptical Basis Function Network, Markov Chain, Missing Covariates, Remaining Useful Life

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Authors: Ephraim Gower, Thato Tsalaile, Monageng Kgwadi, Malcolm Hawksford.

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This paper introduces a new point estimation algorithm, with particular focus on coherent noise suppression, given several measurements of the device under test where it is assumed that 1) the noise is first-order stationery and 2) the device under test is linear and time-invariant. The algorithm exploits the robustness of the Pitman estimator of the Cauchy location parameter through the initial scaling of the test signal by a centred Gaussian variable of predetermined variance. It is illustrated through mathematical derivations and simulation results that the proposed algorithm is more accurate and consistently robust to outliers for different tailed density functions than the conventional methods of sample mean (coherent averaging technique) and sample median search.

Keywords: Central limit theorem, Fisher-Cramer Rao, gamma function, Pitman estimator.

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Authors: Abdenour Bounsiar, Edith Grall, Pierre Beauseroy

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In this paper we are interested in classification problems with a performance constraint on error probability. In such problems if the constraint cannot be satisfied, then a rejection option is introduced. For binary labelled classification, a number of SVM based methods with rejection option have been proposed over the past few years. All of these methods use two thresholds on the SVM output. However, in previous works, we have shown on synthetic data that using thresholds on the output of the optimal SVM may lead to poor results for classification tasks with performance constraint. In this paper a new method for supervised classification with rejection option is proposed. It consists in two different classifiers jointly optimized to minimize the rejection probability subject to a given constraint on error rate. This method uses a new kernel based linear learning machine that we have recently presented. This learning machine is characterized by its simplicity and high training speed which makes the simultaneous optimization of the two classifiers computationally reasonable. The proposed classification method with rejection option is compared to a SVM based rejection method proposed in recent literature. Experiments show the superiority of the proposed method.

Keywords: rejection, Chow's rule, error-reject tradeoff, SupportVector Machine.

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Authors: Manisha Chaudhary, Joydip Dhar, Govind Prasad Sahu

Abstract:

A mathematical model is proposed considering the forest biomass density B(t), density of wood based industries W(t) and density of synthetic industries S(t). It is assumed that the forest biomass grows logistically in the absence of wood based industries, but depletion of forestry biomass is due to presence of wood based industries. The growth of wood based industries depends on B(t), while S(t) grows at a constant rate, independent of B(t). Further there is a competition between W(t) and S(t) according to market demand. The proposed model has four ecologically feasible steady states, namely, E1: forest biomass free and wood industries free equilibrium; E2: wood industries free equilibrium and two coexisting equilibria E∗1 , E∗2 . Behavior of the system near all feasible equilibria is analyzed using the stability theory of differential equations. In the proposed model, the natural depletion rate h1 is a crucial parameter and system exhibits Hopf-bifurcation about the non-trivial equilibrium with respect to h1. The analytical results are verified using numerical simulation.

Keywords: A mathematical model, Competition between wood based and synthetic industries, Hopf-bifurcation, Stability analysis.

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Authors: Noor Zainab Habib, Ibrahim Kamaruddin, Madzalan Napiah, Isa Mohd Tan

Abstract:

This paper presents a part of research on the rheological properties of bitumen modified by thermoplastic namely linear low density polyethylene (LLDPE), high density polyethylene (HDPE) and polypropylene (PP) and its interaction with 80 pen base bitumen. As it is known that the modification of bitumen by the use of polymers enhances its performance characteristics but at the same time significantly alters its rheological properties. The rheological study of polymer modified bitumen (PMB) was made through penetration, ring & ball softening point and viscosity test. The results were then related to the changes in the rheological properties of polymer modified bitumen. It was observed that thermoplastic copolymer shows profound effect on penetration rather than softening point. The viscoelastic behavior of polymer modified bitumen depend on the concentration of polymer, mixing temperature, mixing technique, solvating power of base bitumen and molecular structure of polymer used. PP offer better blend in comparison to HDPE and LLDPE. The viscosity of base bitumen was also enhanced with the addition of polymer. The pseudoplastic behavior was more prominent for HDPE and LLDPE than PP. Best results were obtained when polymer concentration was kept below 3%

Keywords: Polymer modified bitumen, Linear low densitypolyethylene, High density polyethylene, Polypropylene.

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Authors: Tomohiro Hachino, Hitoshi Takata, Shigeru Nakayama, Ichiro Iimura, Seiji Fukushima, Yasutaka Igarashi

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This paper presents a nonparametric identification of continuous-time nonlinear systems by using a Gaussian process (GP) model. The GP prior model is trained by artificial bee colony algorithm. The nonlinear function of the objective system is estimated as the predictive mean function of the GP, and the confidence measure of the estimated nonlinear function is given by the predictive covariance of the GP. The proposed identification method is applied to modeling of a simplified electric power system. Simulation results are shown to demonstrate the effectiveness of the proposed method.

Keywords: Artificial bee colony algorithm, Gaussian process model, identification, nonlinear system, electric power system.

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Authors: Ram N. Singh, Abraham K. George, Dawood N. Al-Namaani

Abstract:

The Euler-s equation of motion is extended to include the viscosity stress tensor leading to the formulation of Navier– Stokes type equation. The latter is linearized and applied to investigate the rotational motion or vorticity in a viscous fluid. Relations for the velocity of viscous waves and attenuation parameter are obtained in terms of viscosity (μ) and the density (¤ü) of the fluid. μ and ¤ü are measured experimentally as a function of temperature for two different samples of light and heavy crude oil. These data facilitated to determine the activation energy, velocity of viscous wave and the attenuation parameter. Shear wave velocity in heavy oil is found to be much larger than the light oil, whereas the attenuation parameter in heavy oil is quite low in comparison to light one. The activation energy of heavy oil is three times larger than light oil.

Keywords: Activation Energy, Attenuation, Crude Oil, Navier- Stokes Equation, Viscosity.

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Authors: Sunita Jahirabadkar, Parag Kulkarni

Abstract:

Many real-world data sets consist of a very high dimensional feature space. Most clustering techniques use the distance or similarity between objects as a measure to build clusters. But in high dimensional spaces, distances between points become relatively uniform. In such cases, density based approaches may give better results. Subspace Clustering algorithms automatically identify lower dimensional subspaces of the higher dimensional feature space in which clusters exist. In this paper, we propose a new clustering algorithm, ISC – Intelligent Subspace Clustering, which tries to overcome three major limitations of the existing state-of-art techniques. ISC determines the input parameter such as є – distance at various levels of Subspace Clustering which helps in finding meaningful clusters. The uniform parameters approach is not suitable for different kind of databases. ISC implements dynamic and adaptive determination of Meaningful clustering parameters based on hierarchical filtering approach. Third and most important feature of ISC is the ability of incremental learning and dynamic inclusion and exclusions of subspaces which lead to better cluster formation.

Keywords: Density based clustering, high dimensional data, subspace clustering, dynamic parameter setting.

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Authors: Xun Ge, Jingju Qian

Abstract:

To investigate some relations between higher mathe¬matics scores in Chinese graduate student entrance examination and calculus (resp. linear algebra, probability statistics) scores in subject's completion examination of Chinese university, we select 20 students as a sample, take higher mathematics score as a decision attribute and take calculus score, linear algebra score, probability statistics score as condition attributes. In this paper, we are based on rough-set theory (Rough-set theory is a logic-mathematical method proposed by Z. Pawlak. In recent years, this theory has been widely implemented in the many fields of natural science and societal science.) to investigate importance of condition attributes with respective to decision attribute and strength of condition attributes supporting decision attribute. Results of this investigation will be helpful for university students to raise higher mathematics scores in Chinese graduate student entrance examination.

Keywords: Rough set, higher mathematics scores, decision attribute, condition attribute.

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Authors: Noriko Hanakawa, Masaki Obana

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A simulation tool is proposed for big-scale projection mapping events. The tool has four main functions based on Mapbox and Unity utilities. The first function is building three-dimensional models of real cities using Mapbox. The second function is movie projections to some buildings in real cities using Unity. The third is a movie sending function from a PC to a virtual projector. The fourth function is mapping movies with fitting buildings. The simulation tool was adapted to a real projection mapping event held in 2019. The event completed, but it faced a severe problem in the movie projection to the target building. Extra tents were set in front of the target building, and the tents became obstacles to the movie projection. The simulation tool developed herein could reconstruct the problems of the event. Therefore, if the simulation tool was developed before the 2019 projection mapping event, the problem of the tents being obstacles could have been avoided using the tool. Moreover, we confirmed that the simulation tool is useful for planning future projection mapping events to avoid various extra equipment obstacles, such as utility poles, planting trees, and monument towers.

Keywords: avoiding obstacles, projection mapping, projector position, real 3D map

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Authors: Shiva Subhedar, Abhishek Jain, Shivin Mittal

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Icons are not merely decorative elements in enterprise applications but very often used because of their many advantages such as compactness, visual appeal, etc. Despite these potential advantages, icons often cause usability problems when they are designed without consideration for their many potential downsides. The aim of the current study was to examine the effect of articulatory distance – the distance between the physical appearance of an interface element and what it actually means. In other words, will the subject find the association of the function and its appearance on the interface natural or is the icon difficult for them to associate with its function. We have calculated response time and quality of identification by varying icon concreteness, the context of usage and subject experience in the enterprise context. The subjects were asked to associate icons (prepared for study purpose) with given function options in context and out of context mode. Response time and their selection were recorded for analysis.

Keywords: Icons, icon concreteness, icon recognition, HCI.

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Authors: O. Eisa, M. Shuhaimi

Abstract:

This paper presents a study on the thermodynamics and transport properties of hot potassium carbonate aqueous system (HPC) using electrolyte non-random two liquid, (ELECNRTL) model. The operation conditions are varied to determine the system liquid phase stability range at the standard and critical conditions. A case study involving 30 wt% K2CO3, H2O standard system at pressure of 1 bar and temperature range from 280.15 to 366.15 K has been studied. The estimated solubility index, viscosity, water activity, and density which obtained from the simulation showed a good agreement with the experimental work. Furthermore, the saturation temperature of the solution has been estimated.

Keywords: Viscosity, Saturation index, Activity coefficient, Density.

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Authors: K. R. Balabiyev, A. O. Kaipbayeva

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The article discusses the legal framework of the government’s environmental function and analyzes the role of the national policy in protection of wetlands. The problem is of interest for it deals with the most important branch of economy – utilization of Kazakhstan’s natural resources, protection of health and environmental wellbeing of the population. Development of a longterm environmental program addressing the protection of wetlands represents the final stage of the government’s environmental policy, and is a relatively new function for the public administration system. It appeared due to the environmental measures that require immediate decisions to be taken. It is an integral part of the effort in the field of management of state-owned natural resource, as well as of the measures aimed at efficient management of natural resources to avoid their early depletion or contamination.

Keywords: Environmental focus, government’s environmental function, protection of wetlands.

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Authors: Manoj Singh, Mumtaz Ahmad Khan, Abdul Hakim Khan

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The object of the present paper is to investigate several general families of bilinear and bilateral generating functions with different argument for the Gauss’ hypergeometric polynomials.

Keywords: Appell’s functions, Gauss hypergeometric functions, Heat polynomials, Kampe’ de Fe’riet function, Laguerre polynomials, Lauricella’s function, Saran’s functions.

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Authors: Zeshan Ahmad, Matteo Zoppi, Rezia Molfino

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The objective of positioning the fixture elements in the fixture is to make the workpiece stiff, so that geometric errors in the manufacturing process can be reduced. Most of the work for optimal fixture layout used the minimization of the sum of the nodal deflection normal to the surface as objective function. All deflections in other direction have been neglected. We propose a new method for fixture layout optimization in this paper, which uses the element strain energy. The deformations in all the directions have been considered in this way. The objective function in this method is to minimize the sum of square of element strain energy. Strain energy and stiffness are inversely proportional to each other. The optimization problem is solved by the sequential quadratic programming method. Three different kinds of case studies are presented, and results are compared with the method using nodal deflections as objective function to verify the propose method.

Keywords: Fixture layout, optimization, strain energy, quadratic programming.

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Authors: B. Skrabic, N. Tomic-Plazibat

Abstract:

In this paper real money demand function is analyzed within multivariate time-series framework. Cointegration approach is used (Johansen procedure) assuming interdependence between money demand determinants, which are nonstationary variables. This will help us to understand the behavior of money demand in Croatia, revealing the significant influence between endogenous variables in vector autoregrression system (VAR), i.e. vector error correction model (VECM). Exogeneity of the explanatory variables is tested. Long-run money demand function is estimated indicating slow speed of adjustment of removing the disequilibrium. Empirical results provide the evidence that real industrial production and exchange rate explains the most variations of money demand in the long-run, while interest rate is significant only in short-run.

Keywords: Cointegration, Long-run equilibrium, Money demand function, Vector error correction model.

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Authors: Min Sun, Zhenyu Liu

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In this paper, a new descent-projection method with a new search direction for monotone structured variational inequalities is proposed. The method is simple, which needs only projections and some function evaluations, so its computational load is very tiny. Under mild conditions on the problem-s data, the method is proved to converges globally. Some preliminary computational results are also reported to illustrate the efficiency of the method.

Keywords: variational inequalities, monotone function, global convergence.

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Authors: R. Fatehi, M.A. Fayazbakhsh, M.T. Manzari

Abstract:

Discretization of spatial derivatives is an important issue in meshfree methods especially when the derivative terms contain non-linear coefficients. In this paper, various methods used for discretization of second-order spatial derivatives are investigated in the context of Smoothed Particle Hydrodynamics. Three popular forms (i.e. "double summation", "second-order kernel derivation", and "difference scheme") are studied using one-dimensional unsteady heat conduction equation. To assess these schemes, transient response to a step function initial condition is considered. Due to parabolic nature of the heat equation, one can expect smooth and monotone solutions. It is shown, however in this paper, that regardless of the type of kernel function used and the size of smoothing radius, the double summation discretization form leads to non-physical oscillations which persist in the solution. Also, results show that when a second-order kernel derivative is used, a high-order kernel function shall be employed in such a way that the distance of inflection point from origin in the kernel function be less than the nearest particle distance. Otherwise, solutions may exhibit oscillations near discontinuities unlike the "difference scheme" which unconditionally produces monotone results.

Keywords: Heat conduction, Meshfree methods, Smoothed ParticleHydrodynamics (SPH), Second-order derivatives.

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Authors: Jiann-Ming Wu, Hsiao-Chang Chen, Chun-Chang Wu, Pei-Hsun Hsu

Abstract:

This work explores blind image deconvolution by recursive function approximation based on supervised learning of neural networks, under the assumption that a degraded image is linear convolution of an original source image through a linear shift-invariant (LSI) blurring matrix. Supervised learning of neural networks of radial basis functions (RBF) is employed to construct an embedded recursive function within a blurring image, try to extract non-deterministic component of an original source image, and use them to estimate hyper parameters of a linear image degradation model. Based on the estimated blurring matrix, reconstruction of an original source image from a blurred image is further resolved by an annealed Hopfield neural network. By numerical simulations, the proposed novel method is shown effective for faithful estimation of an unknown blurring matrix and restoration of an original source image.

Keywords: Blind image deconvolution, linear shift-invariant(LSI), linear image degradation model, radial basis functions (rbf), recursive function, annealed Hopfield neural networks.

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Authors: Nasser Mohamed Ramli, Mohamad Syafiq Mohamad

Abstract:

Many types of controllers were applied on the continuous stirred tank reactor (CSTR) unit to control the temperature. In this research paper, Proportional-Integral-Derivative (PID) controller are compared with Fuzzy Logic controller for temperature control of CSTR. The control system for temperature non-isothermal of a CSTR will produce a stable response curve to its set point temperature. A mathematical model of a CSTR using the most general operating condition was developed through a set of differential equations into S-function using MATLAB. The reactor model and S-function are developed using m.file. After developing the S-function of CSTR model, User-Defined functions are used to link to SIMULINK file. Results that are obtained from simulation and temperature control were better when using Fuzzy logic control compared to PID control.

Keywords: CSTR, temperature, PID, fuzzy logic.

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Authors: Paola Lecca, Lorenzo Dematte, Corrado Priami

Abstract:

The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work a mathematical treatment of diffusion that can be incorporated in a stochastic algorithm simulating the dynamics of a reaction-diffusion system is presented. The movement of a molecule A from a region i to a region j of the space is represented as a first order reaction Ai k- ! Aj , where the rate constant k depends on the diffusion coefficient. The diffusion coefficients are modeled as function of the local concentration of the solutes, their intrinsic viscosities, their frictional coefficients and the temperature of the system. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the intrinsic reaction kinetics and diffusion dynamics. To demonstrate the method the simulation results of the reaction-diffusion system of chaperoneassisted protein folding in cytoplasm are shown.

Keywords: Reaction-diffusion systems, diffusion coefficient, stochastic simulation algorithm.

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